LTQ Orbitrap Discovery Hardware Manual

LTQ Orbitrap Discovery Hardware Manual Revision A - 122 5850 For Research Use Only Not for use in Diagnostic Procedures Part of Thermo Fisher Scientific

LTQ Orbitrap Discovery Hardware Manual Revision A - 122 5850 For Research Use Only Not for use in Diagnostic Procedures

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Read This First Welcome to the Thermo Scientific, LTQ Orbitrap Discovery system! The LTQ Orbitrap Discovery is a member of the family of LTQ mass spectrometer (MS) hybrid instruments. Who uses this Guide Scope of this Guide This LTQ Orbitrap Discovery Hardware Manual is intended for all personnel that need a thorough understanding of the instrument (to perform maintenance or troubleshooting, for example). This manual should be kept near the instrument to be available for quick reference. This LTQ Orbitrap Discovery Hardware Manual contains a description of the modes of operation and principle hardware components of your LTQ Orbitrap Discovery instrument. In addition, this manual provides step-by-step instructions for cleaning and maintaining your instrument. This manual includes the following chapters: Chapter 1: Functional Description describes the principal components of the LTQ Orbitrap Discovery. Chapter 2: Basic System Operations provides procedures for shutting down and starting up the LTQ Orbitrap Discovery. Chapter 3: User Maintenance outlines the maintenance procedures that you should perform on a regular basis to maintain optimum MS detector performance. Chapter 4: Replaceable Parts lists the replaceable parts for the MS detector and data system. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual i

Read This First Changes to the Manual Changes to the Manual To suggest changes to this manual, please send your comments to: Editors, Technical Documentation Thermo Fisher Scientific Hanna-Kunath-Str. 11 28199 Bremen Germany documentation.bremen@thermofisher.com You are encouraged to report errors or omissions in the text or index. Thank you. ii LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Read This First Typographical Conventions Typographical Conventions Typographical conventions have been established for Thermo Fisher Scientific manuals for the following: Data input Admonitions Topic headings Data Input Throughout this manual, the following conventions indicate data input and output via the computer: Messages displayed on the screen are represented by capitalizing the initial letter of each word and by italicizing each word. Input that you enter by keyboard is identified by quotation marks: single quotes for single characters, double quotes for strings. For brevity, expressions such as choose File > Directories are used rather than pull down the File menu and choose Directories. Any command enclosed in angle brackets < > represents a single keystroke. For example, press <F1> means press the key labeled F1. Any command that requires pressing two or more keys simultaneously is shown with a plus sign connecting the keys. For example, press <Shift> + <F1> means press and hold the <Shift> key and then press the <F1> key. Any button that you click on the screen is represented in bold face letters. For example, click on Close. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual iii

Read This First Typographical Conventions Admonitions Admonitions contain information that is important, but not part of the main flow of text. Admonitions can be of the following types: Note information that can affect the quality of your data. In addition, notes often contain information that you might need if you are having trouble. Caution information necessary to protect your instrument from damage. Warning hazards to human beings. Each Warning is accompanied by a Warning symbol. Topic Headings The following headings are used to show the organization of topics within a chapter: Chapter Name The following headings appear in the left column of each page: Second Level Topics Third Level Topics Fourth Level Topics iv LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Read This First Safety and EMC Information Safety and EMC Information In accordance with our commitment to customer service and safety, this instrument has satisfied the requirements for the European CE Mark including the Low Voltage Directive. Designed, manufactured and tested in an ISO9001 registered facility, this instrument has been shipped to you from our manufacturing facility in a safe condition. Caution This instrument must be used as described in this manual. Any use of this instrument in a manner other than described here may result in instrument damage and/or operator injury. Identifying Safety Information The LTQ Orbitrap Discovery Hardware Manual contains precautionary statements that can prevent personal injury, instrument damage, and loss of data if properly followed. Warning symbols alert the user to check for hazardous conditions. These appear throughout the manual, where applicable, and are defined in Table i. Table i. Warning Symbols Symbol Description General This general symbol indicates that a hazard is present, which if not avoided, could result in injuries. The source of danger is described in the accompanying text. Electric Shock High voltages capable of causing personal injury are used in the instrument. The instrument must be shut down and disconnected from line power before service or repair work is performed. Noxious This symbol alerts to hazards resulting from noxious fumes. Hot Surface / Heat Allow heated components to cool down before servicing them! Instrument-Specific Hazards Every instrument has specific hazards, so be sure to read and comply with the following precautions. They will help ensure the safe, long-term use of your system. 1. Before plugging in any of the instrument modules or turning on the power, always make sure that the voltage and fuses are set appropriately for your local line voltage. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual v

Read This First Safety and EMC Information 2. Only use fuses of the type and current rating specified. Do not use repaired fuses and do not short-circuit the fuse holder. 3. The supplied power cord must be inserted into a power outlet with a protective earth contact (ground). When using an extension cord, make sure that the cord also has an earth contact. 4. Do not change the external or internal grounding connections. Tampering with or disconnecting these connections could endanger you and/or damage the system. Caution The instrument is properly grounded in accordance with regulations when shipped. You do not need to make any changes to the electrical connections or to the instrument s chassis to ensure safe operation. 5. Never run the system without the housing on. Permanent damage can occur. 6. Do not turn the instrument on if you suspect that it has incurred any kind of electrical damage. Instead, disconnect the power cord and contact a Service Representative for a product evaluation. Do not attempt to use the instrument until it has been evaluated. (Electrical damage may have occurred if the system shows visible signs of damage, or has been transported under severe stress.) 7. Damage can also result if the instrument is stored for prolonged periods under unfavorable conditions (e.g., subjected to heat, water, etc.). 8. Always disconnect the power cord before attempting any type of maintenance. 9. Capacitors inside the instrument may still be charged even if the instrument is turned off. 10. Never try to repair or replace any component of the system that is not described in this manual without the assistance of your service representative. vi LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Read This First Safety and EMC Information Safety Advice for Possible Contamination Hazardous Material Might Contaminate Certain Parts of Your System During Analysis. In order to protect our employees, we ask you to adhere to special precautions when returning parts for exchange or repair. If hazardous materials have contaminated mass spectrometer parts, Thermo Fisher Scientific can only accept these parts for repair if they have been properly decontaminated. Materials, which due to their structure and the applied concentration might be toxic or which in publications are reported to be toxic, are regarded as hazardous. Materials that will generate synergetic hazardous effects in combination with other present materials are also considered hazardous. Your signature on the Repair-Covering letter confirms that the returned parts have been decontaminated and are free of hazardous materials. The Repair-Covering letter can be ordered from your service engineer or downloaded from the Customer Information Service (CIS) site. Please register under http://register.thermo-bremen.com/form/cis. Parts contaminated by radioisotopes are not subject to return to Thermo Fisher Scientific either under warranty or the exchange part program. If parts of the system may be possibly contaminated by hazardous material, please make sure the Field engineer is informed before the engineer starts working on the system. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual vii

Contents Chapter 1 Functional Description...1-1 General Description... 1-2 Specifications... 1-5 Control Elements... 1-6 System Status LEDs... 1-6 Control Panels... 1-7 Linear Ion Trap... 1-12 Orbitrap Analyzer... 1-13 Measuring Principle... 1-13 Curved Linear Trap... 1-13 Extraction of Ion Packets... 1-14 Ion Detection... 1-15 Active Temperature Control... 1-17 HCD Collision Cell... 1-17 Vacuum System... 1-19 Turbopumps... 1-20 Forevacuum Pumps... 1-21 Vacuum System Controls... 1-22 Vacuum System Heating during a System Bakeout... 1-23 Gas Supply... 1-24 Vent Valve of the Linear Ion Trap... 1-26 Cooling Water Circuit... 1-27 Recirculating Chiller... 1-28 Properties of Cooling Water... 1-28 Printed Circuit Boards... 1-29 Linear Ion Trap Electronics... 1-30 Electronic Boards at the Right Side of the Instrument.. 1-31 Electronic Boards on the Left Side of the Instrument... 1-44 Chapter 2 Basic System Operations...2-1 Shutting Down the System in an Emergency... 2-2 Behavior of the System in Case of a Main Failure... 2-2 Placing the System in Standby Condition... 2-4 Shutting Down the System... 2-5 Starting Up the System after a Shutdown... 2-7 Starting Up the Instrument... 2-7 Setting Up Conditions for Operation... 2-8 Resetting the System... 2-10 Resetting the Tune and Calibration Parameters to their Default Values... 2-11 Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual ix

Contents Chapter 3 User Maintenance... 3-1 General Remarks... 3-2 Returning Parts... 3-2 Cleaning the Surface of the Instrument... 3-3 Baking Out the System... 3-4 Bakeout Procedure... 3-4 Maintaining the Vacuum System... 3-6 Exchanging the Lubricant Reservoir of the Turbopumps 3-6 Maintenance of the Recirculating Chiller... 3-7 Reservoir... 3-7 Fluid Bag Filter... 3-7 Condenser Filter... 3-7 Chapter 4 Replaceable Parts... 4-1 Parts Basic System... 4-2 Parts Orbitrap Analyzer... 4-3 Parts Pumping System Orbitrap... 4-3 Parts Gas and Water Supply... 4-5 Electronic Parts... 4-7 Electronics - Right Panel... 4-7 Electronics - Left Panel... 4-8 Electronics Analyzer... 4-8 Electronics Main Supply... 4-9 Glossary... G-1 Index...I-1 x LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Figures LTQ Orbitrap Discovery front view... 1-2 Schematic view of the LTQ Orbitrap Discovery... 1-3 Top lid opened... 1-4 System status LEDs... 1-6 Right side of the LTQ Orbitrap Discovery... 1-7 Upper control panel... 1-8 Power control panel with power control LEDs and switches... 1-9 Main power switch... 1-10 External connections to the LTQ Orbitrap Discovery... 1-11 Schematic view of the Orbitrap cell and example of a stable ion trajectory... 1-13 Layout of the instrument, also showing the applied voltages... 1-14 Principle of electrodynamic squeezing of ions in the Orbitrap as the field strength is increased... 1-15 Approximate shape of ion packets of different m/q after stabilization of voltages... 1-16 HCD collision cell and C-Trap... 1-17 Schematical view of vacuum system (C-Trap compartment not shown)... 1-19 Vacuum components on the left instrument side... 1-20 Vacuum components on the right instrument side... 1-20 Forepumps cabinet... 1-21 Schematical view of the gas supply... 1-24 Valve for HCD collision gas... 1-25 Nitrogen pressure regulator and gas flow divider... 1-26 Schematical view of cooling water circuit... 1-27 Electronic connections to linear trap (covers removed)... 1-30 Electronic boards on the right side of the instrument... 1-31 Preamplifier board... 1-32 Data Acquisition unit (covers removed)... 1-33 Data Acquisition Digital PCI board... 1-34 Data Acquisition Analog board... 1-35 Instrument Control board... 1-37 Power Distribution board... 1-38 Power Supply 1 board... 1-43 Electronic boards on the left side of the instrument... 1-44 Ion Optic Supply board... 1-45 Central Electrode Pulser board... 1-46 Temperature Controller board... 1-47 CLT RF unit (cover removed)... 1-49 Central Electrode Power Supply board... 1-50 High Voltage Power Supply board (cover removed)... 1-52 High Voltage Power Supply board with SPI Bus Termination board.. 1-53 Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual xi

Figures Main power switch in Off position... 2-2 Bakeout timer... 3-4 xii LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Tables System status LEDs of the LTQ Orbitrap Discovery... 1-6 Circuit breakers of the LTQ Orbitrap Discovery... 1-8 Diagnostic LEDs on the Preamplifier board... 1-33 Diagnostic LEDs of the Data Acquisition Digital PCI board... 1-35 Diagnostic LEDs of the Data Acquisition Analog board... 1-36 Diagnostic LEDs of the Power Supply 2 board... 1-36 Diagnostic LEDs of the Instrument Control board... 1-37 Software status LEDs of the Instrument Control board... 1-38 Status LEDs of the Power Distribution board... 1-40 Working modes of the Power Distribution board... 1-41 Operating states of the Power Distribution board... 1-41 Diagnostic LEDs of the Power Supply 1 board... 1-43 Diagnostic LEDs of the Ion Optic Supply board... 1-46 Diagnostic LEDs of the Central Electrode Pulser board... 1-47 Diagnostic LEDs of the Temperature Controller board... 1-48 Diagnostic LEDs of the CLT RF Main board... 1-49 Diagnostic LEDs of the Central Electrode Power Supply board... 1-51 Diagnostic LEDs of the High Voltage Power Supply board... 1-53 User maintenance procedures... 3-2 Parts for the LTQ Orbitrap Discovery... 4-1 Parts LTQ Orbitrap Discovery; 50 Hz (P/N 072 3720)... 4-1 Parts basic system Orbitrap-2 (P/N 122 4790)... 4-2 Parts Upgrade kit Orbitrap HCD option (P/N 122 4800)... 4-2 Parts Orbitrap Installation Kit (P/N 118 8120)... 4-2 Parts Orbitrap-2 chamber; complete (P/N 122 4780)... 4-3 Parts pumping system Orbitrap (P/N 118 4490)... 4-3 Parts pump kit Orbitrap (P/N 117 5000)... 4-3 Parts pump system Orbitrap (P/N 117 5010)... 4-4 Parts gas supply (P/N 117 7881)... 4-5 Upgrade kit gas supply LTQ Orbitrap XL (P/N 122 4820)... 4-5 Parts water supply (P/N 117 8460)... 4-6 Kit gas-water assembly (P/N 208 7351)... 4-6 Electronic parts Orbitrap-2 (P/N 800 1110)... 4-7 Parts Orbitrap-2 electronics; right panel (P/N 208 1010)... 4-7 Parts Unit data acquisition (P/N 206 4132)... 4-8 Parts Orbitrap-2 electronics; left panel (P/N 208 1020)... 4-8 Parts electronics analyzer Orbitrap-2 (P/N 210 0160)... 4-8 Parts electronics main supply Orbitrap (P/N 208 1040)... 4-9 Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual xiii

Chapter 1 Functional Description This chapter provides an overview of the functional elements of the LTQ Orbitrap Discovery. It contains the following topics: General Description on page 1-2 Control Elements on page 1-6 Linear Ion Trap on page 1-12 Orbitrap Analyzer on page 1-13 Vacuum System on page 1-19 Gas Supply on page 1-24 Cooling Water Circuit on page 1-27 Printed Circuit Boards on page 1-29 Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-1

Functional Description General Description General Description LTQ Orbitrap Discovery is a hybrid mass spectrometer incorporating the LTQ XL linear trap and the Orbitrap. Figure 1-1 shows a front view of the instrument. LTQ XL Linear Ion Trap Figure 1-1. LTQ Orbitrap Discovery front view Figure 1-2 on page 1-3 shows the schematic view of the LTQ Orbitrap Discovery. The LTQ Orbitrap Discovery consists of three main components, which are described in the following topics: A linear ion trap (Thermo Scientific LTQ XL) for sample ionization, selection, fragmentation, and AGC. An intermediate storage device (curved linear trap) that is required for short pulse injection. An Orbitrap analyzer for Fourier transformation based analysis. A collision cell for performing HCD (Higher Energy Collisional Dissociation) experiments is available as option for LTQ Orbitrap Discovery. The feature will be not available if the instrument is not equipped with this option. 1-2 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

1 C-Trap HCD collision cell 1 Lens stack Figure 1-2. Schematic view of the LTQ Orbitrap Discovery 1 HCD is an option for LTQ Orbitrap Discovery. The feature will be not available if the instrument is not equipped with this option. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-3

Functional Description General Description Wheels at the bottom side of the instrument facilitate positioning the LTQ Orbitrap Discovery at the intended place in the laboratory. The instrument is designed to be placed with its rear panel against a wall. To ensure a sufficient air flow for cooling the instrument, spacers on the rear panel provide for minimum distance to the wall. The mains inlet as well as a power outlet for peripheral devices (data system, for example) are located at the right side of the instrument. Rotary pumps are hidden under the linear trap and accessible from the front. The left side panel and the front panel are mounted on hinges and the right side panel is removable. The top lid opens upwards to allow easy access for Field Engineers from the top. See Figure 1-3. Figure 1-3. Top lid opened A stand-alone recirculating water chiller is delivered with the instrument. It is connected to the right side of the instrument. 1-4 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Functional Description General Description Specifications The LTQ Orbitrap Discovery has the following measuring properties: Resolution (apodized)30000 (FWHM) @ m/z 400 with a detect time of 400 ms Minimum resolution 7500, maximum resolution 30000 @ m/z 400 Mass Range m/z 50 2000; m/z 200 4000 Mass Accuracy Dynamic Range MS/MS <5 ppm RMS for 8 h period with external calibration, <2 ppm RMS with internal calibration >10000 between mass spectra, >4000 between highest and lowest detectable mass in one spectrum MS/MS and MS n scan functions Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-5

Functional Description Control Elements Control Elements The LTQ Orbitrap Discovery is mainly operated from the desktop computer (data system). Some control elements for important system functions are located directly on the instrument. They are described in the following sections. System Status LEDs Figure 1-4 shows the system status LEDs at the front of the instrument. Five LEDs indicate the main functions of the system. (See also Figure 1-5 on page 1-7.) While the Power LED is directly controlled by the 3 230 V input, all other LEDs are controlled by the power distribution board (Refer to topic Power Distribution Board on page 1-38). Table 1-1 explains the function of the various LEDs. Figure 1-4. System status LEDs The system status LEDs at the front panel of the linear ion trap are described in the LTQ XL Hardware Manual. Table 1-1. System status LEDs of the LTQ Orbitrap Discovery LED Status Information Power Green Off Main switch on Main switch off Vacuum * Green Operating vacuum reached Yellow Insufficient vacuum or Vacuum Pumps switch off Communication Green Communication link between instrument and data system established Yellow Communication link starting up or Vacuum Pumps switch off System * Green System ready Yellow FT Electronics switch off or Vacuum Pumps switch off Detect Blue Instrument is scanning Off Instrument is not scanning * These LEDs are flashing when a system bakeout is performed. See topic Baking Out the System on page 3-4. 1-6 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Functional Description Control Elements Control Panels Figure 1-5 shows the right side of the LTQ Orbitrap Discovery. Located here are the control panels, switches, and the ports for the external connections (mains supply, gases, Ethernet communication, and cooling water). System status LEDs of linear trap System status LEDs of LTQ Orbitrap Discovery Bakeout timer Cover lid for bake out controls Switches and control LEDs Main power switch Power connector Forepumps cabinet Power panel of linear trap Figure 1-5. Right side of the LTQ Orbitrap Discovery For more information about the external connections, refer to topic External Connections on page 1-10. Upper Control Panel The upper instrument control panel comprises the bakeout timer, the bakeout control buttons, and three circuit breakers. To access the upper control panel, swing open the small lid (opens from left to right). See Figure 1-5 and Figure 1-6 on page 1-8. The timer allows setting the duration for the bakeout of the system. After the duration is set, the bakeout procedure is started by pressing the green button on the right. A running bakeout procedure can be stopped by pressing the orange button on the left side. For instructions about performing a bakeout, refer to topic Baking Out the System on page 3-4. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-7

Functional Description Control Elements Bakeout timer Cover lid Bakeout control buttons Circuit breakers Figure 1-6. Upper control panel Note The buttons themselves have no indicator function. A running bakeout procedure is indicated by flashing Vacuum and System LEDs at the front side of the instrument. See Figure 1-4 on page 1-6. Three circuit breakers are located at the bottom of this control panel. Table 1-2 shows the parts of the LTQ Orbitrap Discovery that are protected by the respective circuit breaker. The proper function of each circuit breaker is signaled by a dedicated LED in the power control panel (for example, F1 corresponds to L1). Table 1-2. Circuit breakers of the LTQ Orbitrap Discovery Circuit breaker Ampere LED Instrument parts F1 10 L1 Power Distribution F2 16 L2 Linear ion trap F3 10 L3 Multiple socket outlets (Data system, LC, heater, etc.) Power Control Panel In addition to the system status LEDs at the front side (see Figure 1-4 on page 1-6), the LTQ Orbitrap Discovery has three power control LEDs above the Vacuum Pumps switch at the right side. See Figure 1-7. They indicate whether the corresponding circuit breaker is closed and the respective parts of the instrument have power. (See Table 1-2 on page 1-8.) 1-8 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Functional Description Control Elements Power control LEDs Vacuum Pumps switch FT Electronics switch Figure 1-7. Power control panel with power control LEDs and switches The use of the switches below the power control LEDs changes the working mode of the power distribution. (See topic Working Modes of the Power Distribution on page 1-48.) The Vacuum Pumps switch can be set into the positions ON or OFF. When the switch is in the OFF position, everything but the multiple socket outlet is switched off. The FT Electronics switch can be set into the Operating Position (ON) or into the Service Position (OFF). When the switch is in the Service position, all components are switched off with exception of the following: Fans Heater control Power distribution (Refer to the topic Power Distribution Board on page 1-38) Pumps (Refer to the topic Vacuum System on page 1-19) Temperature controller (Refer to the topic Temperature Controller Board on page 1-47) Vacuum control The linear ion trap also remains on because it has a separate Service switch. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-9

Functional Description Control Elements Main Power Switch The main power switch must be turned 90 clockwise/anti-clockwise to switch on/off the instrument (see Figure 1-8). Placing the main power switch in the Off position turns off all power to the LTQ Orbitrap Discovery (and linear ion trap as well, including the vacuum pumps). On Off Figure 1-8. Main power switch Note When the main power switch is in the Off position, you can secure it with a padlock or a cable tie (to prevent unintended re-powering when performing maintenance, for example). External Connections Figure 1-9 on page 1-11 shows the lower right side of the instrument with the external connections for mains supply, gases, cooling water, and Ethernet communication. The power connector for the mains supply is located on the center. The cooling water ports are located below the power connector. (See also topic Cooling Water Circuit on page 1-27.) A Teflon hose connects the instrument to the nitrogen gas supply. An analogous port is used for the HCD collision gas supply. 1 Metal tubing connects the instrument with the helium gas supply. (See also topic Gas Supply on page 1-24.) Located at the top are two ports for Ethernet cables for connecting the LTQ Orbitrap Discovery and the linear ion trap via an Ethernet hub with the data system computer. The exhaust hose from the rotary pumps is led backwards below the instrument, comes out the back of the instrument, and connects the pumps to the exhaust system in the laboratory. 1 HCD is an option for LTQ Orbitrap Discovery. The feature will be not available if the instrument is not equipped with this option. 1-10 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Functional Description Control Elements 1 Ethernet ports Power outlet for peripheral devices Power connector Helium gas inlet Collision gas inlet 1 Inlet for nitrogen gas Cooling water inlet port Cooling water outlet port Figure 1-9. External connections to the LTQ Orbitrap Discovery The power outlet for peripheral devices (data system, for example) is located above the mains supply port. The outlet provides the mains supply for the peripherals via a multiple socket outlet. Caution Do not connect the recirculating chiller to the peripherals power outlet! Furthermore, make sure that the maximum current drawn from the power outlet does not exceed 16 A. Overloading it (by connecting to many pieces of equipment to the multiple socket outlet, for example) may destroy the outlet by excessive heating. 1 Not used in the standard version of the LTQ Orbitrap Discovery. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-11

Functional Description Linear Ion Trap Linear Ion Trap The LTQ Orbitrap Discovery system can utilize a variety of ionization techniques such as ESI, APCI, or APPI. Maintenance of the API source, as well as switching between ionization methods, is vent-free. Ions are transferred by octapole and square quadrupole lenses into an ion trap that is optimized for axial ion ejection into the curved linear trap. (See Figure 1-2 on page 1-3.) The linear ion trap is an independent MS detector (Thermo Scientific LTQ XL), which can store, isolate, and fragment ions and then send them either to the Orbitrap for further analysis or to an SEM detector. The linear ion trap is a unique ion preparation and injection system for Orbitrap MS, because it has greater ion storage capacity than conventional 3D ion trap devices. The linear ion trap is completely described in the LTQ XL Hardware Manual. All the ion handling, selection and excitation capabilities of the ion trap can be used to prepare ions for analysis in the Orbitrap. These features include storage and ejection of all ions, storage of selected masses or mass ranges, as well as ion isolation. Isolated ions can be excited and then fragmented as necessary for MS/MS and MSn experiments. The patented Automatic Gain Control (AGC) provides extended dynamic range and insures optimized overall performance of the ion trap and Orbitrap MS. The linear ion trap and the transfer chamber are mounted on a table. See Figure 1-1 on page 1-2. The table also serves as a housing for the forepumps. See Figure 1-18 on page 1-21. The LTQ Orbitrap Discovery provides power for the linear ion trap and for the data system. The linear ion trap is delivered with power connector, gas lines (He, N 2, and collision gas), and vacuum tube lines extending to the ESI source. On the rear side of the LTQ XL ion trap is a flange with an O-ring seal. When the flange is removed, the Orbitrap transfer chamber is mounted to the flange of the linear ion trap. The transfer chamber is held with supports on the table. The components of the ion optics and the Orbitrap are fixed to the transfer chamber. 1-12 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Functional Description Orbitrap Analyzer Orbitrap Analyzer This section describes the basic principle of the Orbitrap analyzer. The heart of the system is an axially-symmetrical mass analyzer. It consists of a spindle-shape central electrode surrounded by a pair of bell-shaped outer electrodes. See Figure 1-10. The Orbitrap employs electric fields to capture and confine ions. Figure 1-10. Schematic view of the Orbitrap cell and example of a stable ion trajectory Measuring Principle In the mass analyzer shown in Figure 1-10, stable ion trajectories rotate around an axial central electrode with harmonic oscillations along it. The frequency ω of these harmonic oscillations along the z-axis depends only on the ion mass-to-charge ratio m/q and the instrumental constant k: w = q m --- k Two split halves of the outer electrode of the Orbitrap detect the image current produced by the oscillating ions. By Fast Fourier Transformation (FFT) of the image current, the instrument obtains the frequencies of these axial oscillations and therefore the mass-to-charge ratios of the ions. Curved Linear Trap On their way from the linear trap to the Orbitrap, ions move through the gas-free RF octapole (Oct 1) into the gas-filled curved linear trap (C-Trap). See Figure 1-11 on page 1-14. Ions in the C-Trap are returned by the trap electrode. Upon their passage, the ions loose enough kinetic energy to prevent them from leaving the C-Trap through the Gate. The nitrogen collision gas (bath gas) is used for dissipating the kinetic energy of ions injected from the LTQ XL and for cooling them down to the axis of the curved linear trap. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-13

Functional Description Orbitrap Analyzer Voltages on the end apertures of the curved trap (Trap and Gate apertures) are elevated to provide a potential well along its axis. These voltages may be later ramped up to squeeze ions into a shorter thread along this axis. The RF to the C-Trap ( Main RF ) is provided by the CLT RF main board. (See page 1-48.) Trap and gate DC voltages as well as RF voltages to octapole 1 are all provided by the ion optic supply board. (See page 1-45.) High voltages to the lenses are provided by the high voltage power supply board. (See page 1-51.) 1 HCD collision octapole 1 Figure 1-11. Layout of the instrument, also showing the applied voltages Extraction of Ion Packets For ion extraction, the RF on the rods of the C-Trap is switched off and extracting voltage pulses are applied to the electrodes, pushing ions orthogonally to the curved axis through a slot in the inner hyperbolic electrode. Because of the initial curvature of the curved trap and the subsequent lenses, the ion beam converges on the entrance into the Orbitrap. The lenses form also differential pumping slots and cause spatial focusing of the ion beam into the entrance of the Orbitrap. Ions are electrostatically deflected away from the gas jet, thereby eliminating gas carryover into the Orbitrap. 1 HCD is an option for LTQ Orbitrap Discovery. The feature will be not available if the instrument is not equipped with this option. 1-14 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Functional Description Orbitrap Analyzer Owing to the fast pulsing of ions from the curved trap, ions of each mass-to-charge ratio arrive at the entrance of the Orbitrap as short packets only a few millimeters long. For each mass/charge population, this corresponds to a spread of flight times of only a few hundred nanoseconds for mass-to-charge ratios of a few hundred Daltons/charge. Such durations are considerably shorter than a half-period of axial ion oscillation in the trap. When ions are injected into the Orbitrap at a position offset from its equator (Figure 1-12), these packets start coherent axial oscillations without the need for any additional excitation cycle. Figure 1-12. Principle of electrodynamic squeezing of ions in the Orbitrap as the field strength is increased The evolution of an ion packet during the increase of the electric field is shown schematically on Figure 1-12. When the injected ions approach the opposite electrode for the first time, the increased electric field (owing to the change of the voltage on the central electrode) contracts the radius of the ion cloud by a few percent. The applied voltages are adjusted to prevent collision of the ions with the electrode. A further increase of the field continues to squeeze the trajectory closer to the axis, meanwhile allowing for newly arriving ions (normally, with higher m/q) to enter the trap as well. After ions of all m/q have entered the Orbitrap and moved far enough from the outer electrodes, the voltage on the central electrode is kept constant and image current detection takes place. Ion Detection During ion detection, both the central electrode and deflector are maintained at very stable voltages so that no mass drift can take place. The outer electrode is split in half at z=0, allowing the ion image current in the axial direction to be collected. The image current on each of half of the outer electrode is differentially amplified and then undergoes analog-to-digital conversion before processing using the fast Fourier transform algorithm. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-15

Functional Description Orbitrap Analyzer Figure 1-13. Approximate shape of ion packets of different m/q after stabilization of voltages As mentioned above, stable ion trajectories within the Orbitrap combine axial oscillations along the z-axis with rotation around the central electrode and vibrations in the radial direction. (See Figure 1-10 on page 1-13.) For any given m/q, only the frequency of axial oscillations is completely independent of initial ion parameters, while rotational and radial frequencies exhibit strong dependence on initial radius and energy. Therefore, ions of the same mass/charge ratio continue to oscillate along z together, remaining in-phase for many thousands of oscillations. In contrast to the axial oscillations, the frequencies of radial and rotational motion will vary for ions with slightly different initial parameters. This means that in the radial direction, ions dephase orders of magnitude faster than in the axial direction, and the process occurs in a period of only 50 100 oscillations. After this, the ion packet of a given m/q assumes the shape of a thin ring, with ions uniformly distributed along its circumference. (See Figure 1-13.) Because of this angular and radial smearing, radial and rotational frequencies cannot appear in the measured spectrum. Meanwhile, axial oscillations will persist, with axial thickness of the ion ring remaining small compared with the axial amplitude. Moving from one half outer electrode to the other, this ring will induce opposite currents on these halves, thus creating a signal to be detected by differential amplification. 1-16 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Functional Description Orbitrap Analyzer Active Temperature Control Active temperature control is achieved by monitoring temperature directly on the Orbitrap assembly and compensating any changes in ambient temperature by a thermoelectric cooler (Peltier element) on the outside of the UHV chamber. A dedicated temperature controller board is used for this purpose. See page 1-47. Peltier Cooling To allow stable operating conditions in the UHV chamber, it can be cooled or heated (outgassing) by means of a Peltier element located on the outside. A second Peltier element is located on the back of the CE power supply board. See Figure 1-32 on page 1-44. The Peltier cooling is based on the Peltier Effect, which describes the effect by which the passage of an electric current through a junction of two dissimilar materials (thermoelectric materials) causes temperature differential (cooling effect). The voltage drives the heat to flow from one side of the Peltier element to the other side, resulting in cooling effects on one side and heating effects on the other side. To remove the heat from the hot side of the Peltier elements, they are connected to the cooling water circuit of the LTQ Orbitrap Discovery. See topic Cooling Water Circuit on page 1-27 for further information. HCD Collision Cell HCD is an option for LTQ Orbitrap Discovery. The feature will be not available if the instrument is not equipped with this option. HCD collision cell C-Trap Figure 1-14. HCD collision cell and C-Trap Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-17

Functional Description Orbitrap Analyzer The collision cell consists of a straight multipole mounted inside a metal tube which is connected in direct line-of-sight to the C-Trap. Figure 1-14 on page 1-17 shows a close-up view of the configuration. It is supplied with a collision gas through the open split interface, providing increased gas pressure inside the multipole. The choice of collision gas is independent from the gas in the C-Trap. See topic Gas Supply on page 1-24 for details. The front of the tube is equipped with a lens for tuning transmission and ejection to/from the C-Trap. The ion optic supply board provides the voltages for the collision cell. (See page 1-45.) For HCD (Higher Energy Collisional Dissociation), ions are passed through the C-Trap into the collision cell. The offset between the C-Trap and HCD is used to accelerate the parents into the gas-filled collision cell. The fragment spectra generated in the collision cell and detected in the Orbitrap show a fragmentation pattern comparable to the pattern of typical collisional quadrupole spectra. See the LTQ Orbitrap Discovery Getting Started manual for more information. 1-18 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Functional Description Vacuum System Vacuum System Figure 1-15 shows a schematic overview of the vacuum system. The Orbitrap has the following vacuum compartments: CLT compartment in the aluminum vacuum chamber (pumped by the same pump as the linear trap) Vacuum chamber (pumped by a water-cooled 60 L/s for N 2 turbopump TMH 071, TMP 1, manufacturer: Pfeiffer) Ultra high vacuum chamber (UHV chamber, pumped by a water-cooled 60 L/s turbopump TMH 071, TMP 2, manufacturer: Pfeiffer) Orbitrap chamber (pumped by a 210 L/s for N 2 water-cooled turbopump TMU 262, TMP 3, manufacturer: Pfeiffer) The forepumps of the linear trap provide the forevacuum for the turbopumps. LTQ XL UHV Chamber Vacuum Chamber Turbopump TMH 071 (TMP 2) Orbitrap Chamber Pirani Gauge Cold Ion Gauge LTQ XL Fore Pump Fore Pump Turbopump TMU 262 (TMP 3) Turbopump TMH 071 (TMP 1) Figure 1-15. Schematical view of vacuum system (C-Trap compartment not shown) * * For an abridged version of the parts list, see Table 4-7 on page 4-3. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-19

Functional Description Vacuum System Turbopumps All parts of the system except for the Orbitrap analyzer are mounted in a aluminum vacuum chamber evacuated by a 60 L/s turbopump (TMP 1, see Figure 1-16). The rotary vane pumps of the linear trap (see below) provide the forevacuum for this pump. This chamber is bolted to a stainless steel welded UHV chamber housing the Orbitrap, lenses, and corresponding electrical connections. Pirani gauge Turbopump vacuum chamber (TMP 1) Figure 1-16. Vacuum components on the left instrument side The UHV chamber is evacuated down to 10-8 mbar pressure range by a 60 L/s UHV turbopump (TMP 2, see Figure 1-17). 1 Preamplifier HCD housing 1 Cooling water supply for Peltier element Cold Ion Gauge Turbopump TMU 262 (TMP 3) Turbopump TMH 071 (TMP 2) Figure 1-17. Vacuum components on the right instrument side 1 HCD is an option for LTQ Orbitrap Discovery. The feature will be not available if the instrument is not equipped with this option. 1-20 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Functional Description Vacuum System The Orbitrap itself is separated from the UHV chamber by differential apertures and is evacuated down to 10-10 mbar by a 210 L/s turbopump (TMP 3, see Figure 1-17 on page 1-20). All turbopumps are equipped with TC 100 control units (manufacturer: Pfeiffer). Linear Trap Turbopump A separate turbopump provides the high vacuum for the linear ion trap. It it is mounted to the bottom of the vacuum manifold of the linear ion trap. For more information, refer to the LTQ XL Hardware Manual. Forevacuum Pumps The rotary vane pumps from the linear trap serve as forepumps for the two smaller turbopumps (TMP 1 and TMP 2). The exhaust hose from the forepumps is led to the back of the instrument and connects them to the exhaust system in the laboratory. The forepumps are located on a small cart in the forepumps cabinet below the linear trap. See Figure 1-18. Oil mist filters Figure 1-18. Forepumps cabinet Forepumps To minimize the ingress of pump oil into the exhaust system, the outlets of the forepumps are fitted to oil mist filters. See page 3-6 on instructions about returning the collected oil to the forepumps. The forevacuum pumps (forepumps) of the linear trap are powered by the power panel of the linear ion trap. Warning When analyzing hazardous materials, these may be present in the effluent of the forepumps! The connection to an adequate exhaust system is mandatory! Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-21

Functional Description Vacuum System Leave the on/off switches of the forepumps always in the On position to provide the control from the vacuum control panel. Before starting the pumps, however, make sure that: The forevacuum pumps are filled with oil, They are connected to the power supply, and The gas ballast is shut. For a detailed description of the forepumps, refer to the handbook of the manufacturer. Vacuum System Controls The power distribution board controls all turbopumps via voltage levels. Refer to topic Power Distribution Board on page 1-38. An interface for RS485 data via the instrument control board connects the turbopumps with the linear ion trap. (Refer to topic Instrument Control Board on page 1-36.) The linear ion trap has a separate turbopump controller. Vacuum Gauges The vacuum is monitored by several vacuum gauges: The forevacuum of the LTQ Orbitrap Discovery is monitored by an Active Pirani gauge (TPR 280, manufacturer: Pfeiffer) connected to the LTQ Orbitrap Discovery forevacuum line. See photo right and Figure 1-16 on page 1-20. The high vacuum of the LTQ Orbitrap Discovery is monitored by a Cold Ion Gauge (IKR 270, manufacturer: Pfeiffer) connected to the UHV chamber. See Figure 1-17 on page 1-20. Since the gauge would be contaminated at higher pressures, it is only turned on when the forevacuum has fallen below a safety threshold (<10-2 mbar). The linear ion trap vacuum is monitored by a Convectron gauge and an ion gauge. Refer to the LTQ XL Hardware Manual for more information. The vacuum gauges of the LTQ Orbitrap Discovery are connected to the power distribution board that directly responds to the pressure values. (Refer to the topic Power Distribution Board on page 1-38.) 1-22 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Functional Description Vacuum System The analog values are digitized by the instrument control board. (Refer to the topic Instrument Control Board on page 1-36.) They are then sent as readout values to the data system. Switching on the Vacuum System When the vacuum system is switched on, the following occurs: 1. After the Vacuum Pumps switch is switched On, the pumps of the linear ion trap and the LTQ Orbitrap Discovery are run up. The Pirani gauge (see above) controls the LTQ Orbitrap Discovery low vacuum pressure as well as the pressure at the forevacuum pumps. Within a short time, a significant pressure decrease must be observed. The goodness of the vacuum can be estimated by means of the rotation speed of the turbopumps (e.g. 80% after 15 min.). 2. If the working pressure is not reached after the preset time, the complete system is switched off. At the status LED panel of the power distribution board, an error message (Vacuum Failure) is put out (see below). 3. The Cold Ion Gauge is only switched on after the low vacuum is reached. It is then used to monitor the vacuum in the Orbitrap region. Vacuum Failure In case the pressure in the LTQ Orbitrap Discovery or the linear ion trap exceeds a safety threshold, the complete system including linear ion trap, electronics, and pumps is switched off. However, the power distribution is kept under current and puts out an error message at the LED panel. (Refer to the topic Power Distribution Board on page 1-38.) It can be reset by switching the main power switch off and on. (Refer to the topic Main Power Switch on page 1-10.) Upon venting, the vent valves of the turbopumps on the Orbitrap detector stay closed. Only the vent valve of the linear ion trap is used. (Refer to the topic Vent Valve of the Linear Ion Trap on page 1-26.) Vacuum System Heating during a System Bakeout After the system has been open to the atmosphere (e.g. for maintenance work), the vacuum deteriorates due to contaminations of the inner parts of the vacuum system caused by moisture or a power outage. These contaminations must be removed by heating the vacuum system: a system bakeout. Refer to the topic Baking Out the System on page 3-4. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-23

Functional Description Gas Supply Gas Supply Figure 1-19 shows a schematical view of the gas supply in the instrument. The LTQ Orbitrap Discovery uses at least two gases for operation: 1 HCD collision gas 1 Nitrogen, Helium, and Argon (optional as HCD collision gas) 1. Collision gas valve 1 HCD collision cell 1 Figure 1-19. Schematical view of the gas supply * * For parts lists of the gas supply, refer to Table 4-10 on page 4-5. The linear trap requires high-purity (99%) nitrogen for the API sheath gas and auxiliary/sweep gas. The Orbitrap uses nitrogen as collision gas (bath gas) for the curved linear trap. The linear trap requires ultra-high 1 HCD is an option for LTQ Orbitrap Discovery. The feature will be not available if the instrument is not equipped with this option. 1-24 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Functional Description Gas Supply purity (99.999%) helium for the collision gas. Nitrogen is also used as collision gas for the optional HCD octapole. If argon is used as HCD collision gas, it should be of high purity (99.99%). The laboratory gas supply is connected to the inlets at the right side of the instrument. See Figure 1-9 on page 1-11. Within the instrument, the helium gas is led from the helium port through a stainless steel capillary to the right rear side of the linear trap. Nitrogen gas and HCD collision gas are both led via Teflon tubing to the right side of the LTQ Orbitrap Discovery. Part of the nitrogen gas flow is directed through Teflon tubing via a pressure regulator to the vent valve of the linear trap. (See below for further information.) Another part of the nitrogen flow is directed through Teflon tubing to the vacuum chamber of the Orbitrap. Nitrogen gas pressure to the C-Trap is kept constant by using an open-split interface (gas flow divider, see Figure 1-21). It contains a capillary line from the nitrogen line of the instrument to atmosphere (flow rate: ~20 ml/min), with another capillary leading from the point of atmospheric pressure into the C-Trap (flow rate: ~0.2 ml/min). For the nitrogen gas to the C-Trap, black PEEKSil tubing is used (75 μm ID silica capillary in 1/16 in PEEK tubing). Orbitrap CLT RF Main board housing Temperature controller board Figure 1-20. Valve for HCD collision gas Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-25

Functional Description Gas Supply The HCD collision gas is also led to a gas flow divider. Part of the gas is led through a capillary line to the atmosphere (flow rate: ~20 ml/min). The other part of the gas (flow rate: ~0.5 ml/min) enters the IN port of a three way valve. The gas leaves the valve through the OUT port and is led to the collision octapole next to the curved linear trap. 1 For the HCD collision gas, red PEEKSil tubing is used (100 μm ID silica capillary in 1/16 in PEEK tubing). The valve is located at the left instrument side next to the temperature controller board. See Figure 1-20 on page 1-25. It is switched by the software via the power distribution board. (See page 1-38.) Vent Valve of the Linear Ion Trap If the system and pumps are switched off, the system is vented. The vent valve is controlled by the linear ion trap. The LTQ XL Hardware Manual contains further information about the vent valve. The instrument is vented with nitrogen from the same tubing that supplies the LTQ XL sheath gas. See Figure 1-19 above. The vent valve of the LTQ XL is attached to a pressure regulator that is set to a venting pressure of 3 4 psi. The pressure regulator is located at the left side of the LTQ Orbitrap Discovery. See Figure 1-21. Gas flow divider Nitrogen pressure regulator Figure 1-21. Nitrogen pressure regulator and gas flow divider 1 The third port of the valve is closed. 1-26 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Functional Description Cooling Water Circuit Cooling Water Circuit Figure 1-22 on page 1-27 shows a schematical view of the cooling water circuit in the LTQ Orbitrap Discovery. Cooling water at a temperature of 20 C enters and leaves the instrument at the bottom of the right side. See Figure 1-9 on page 1-11. First, the fresh water passes through the turbopumps in the order TMP 3 TMP 1 TMP 2. Then it passes through the heating element (Peltier element) that keeps constant (±0.5 C) the preset temperature of the analyzer. Before it leaves the instrument, the water passes through the other Peltier element at the back of the central electrode power supply board. Figure 1-22. Schematical view of cooling water circuit * * For a parts list of the cooling water circuit, refer to Table 4-12 on page 4-6. A flow control sensor is connected to the power distribution board and allows displaying the current flow rate of the cooling water in the software. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-27

Functional Description Cooling Water Circuit Recirculating Chiller A recirculating chiller (NESLAB Merlin M-33 or NESLAB ThermoFlex 900) is delivered with the instrument, making the LTQ Orbitrap Discovery independent from any cooling water supply. A wall receptacle provides the electric power for the chiller. Two water hoses (black), internal diameter 9 mm, wall thickness 3 mm, length approx. 3 m (~10 ft) are delivered with the instrument. For instruction about performing maintenance for the chiller, see topic Maintenance of the Recirculating Chiller on page 3-7. See also the manufacturer s manual for the chiller. Properties of Cooling Water The water temperature is not critical, but should be in the range of 20 to 25 C (68 to 77 F). Lower temperatures could lead to a condensation of atmospheric water vapor. It is recommended to use distilled water rather than de-ionized water due to lower concentration of bacteria and residual organic matter. The water should be free of suspended matter to avoid clogging of the cooling circuit. In special cases, an in-line filter is recommended to guarantee consistent water quality. The cooling water should meet the following requirements: Hardness: <0.05 ppm Resistivity: 1 3 MΩ/cm Total dissolved solids: <10 ppm ph: 7 8 Warning Danger of Burns! If the water circuit fails, all parts of the water distribution unit may be considerably heated up. Do not touch the parts! Before disconnecting the cooling water hoses, make sure the cooling water has cooled down! 1-28 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Functional Description Printed Circuit Boards Printed Circuit Boards The LTQ Orbitrap Discovery is controlled by a PC running the Xcalibur software suite. The software controls all aspects of the instrument. The main software elements are the communication with the linear ion trap, the control of ion detection, and the control of the Orbitrap mass analyzer. The following pages contain a short overview of the various electronic boards of the LTQ Orbitrap Discovery. For each board, its respective location and function are given. If applicable, the diagnostic LEDs on the board are described. The electronics of the LTQ Orbitrap Discovery contains complicated and numerous circuits. Therefore, only qualified and skilled electronics engineers should perform servicing. A Thermo Fisher Scientific Service Engineer should be called if servicing is required. It is further recommended to use Thermo Fisher Scientific spare parts only. When replacing fuses, only use the correct type. Before calling a Service Engineer, please try to localize the defect via errors indicated in the software or diagnostics. A precise description of the defect will ease the repair and reduce the costs. Warning Parts of the printed circuit boards are at high voltage. Opening the electronics cabinet is only allowed for maintenance purposes by qualified personal. Note Many of the electronic components can be tested by the LTQ Orbitrap Discovery diagnostics, which is accessible from the Tune Plus window. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-29

Functional Description Printed Circuit Boards Linear Ion Trap Electronics The linear ion trap is connected to the LTQ Orbitrap Discovery main power switch. The linear ion trap has a sheet metal back cover. Figure 1-23 shows the electronic connections at the rear side of the linear trap. Cold Ion Gauge Figure 1-23. Electronic connections to linear trap (covers removed) The linear ion trap electronics has two connections with the LTQ Orbitrap Discovery electronics: Data communication with the internal computer of the LTQ Orbitrap Discovery. Refer to the topic Electronic Boards at the Right Side of the Instrument on page 1-31. Signal communication (SPI bus) with supply information for the instrument control board. Refer to the topic Instrument Control Board on page 1-36. For further information about the linear ion trap electronics, refer to the LTQ XL Hardware Manual. 1-30 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Functional Description Printed Circuit Boards Electronic Boards at the Right Side of the Instrument Figure 1-24 shows the parts of the instrument when the right side panel is opened. A transparent cover protects the lower part. Preamplifier Computer housing Instrument Control board housing Power Supply 1 board Power Distribution board Ground wire for side panel Ground wire for side panel Figure 1-24. Electronic boards on the right side of the instrument The side panel is connected to the instrument frame by two green/yellow ground wires. See bottom of Figure 1-24. The connectors on the panel are labeled with green-yellow PE (for Protective Earth) signs. See photo left. Do not forget to reconnect them before closing the panel! Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-31

Functional Description Printed Circuit Boards Preamplifier Figure 1-25 shows the preamplifier (P/N 207 8900) 1. The preamplifier is located in a housing next to the Cold Ion Gauge. Cooling water supply for Peltier element Cold Ion Gauge Figure 1-25. Preamplifier board This board is a broadband preamplifier with differential high-impedance inputs. It serves as a detection amplifier and impedance converter for the image current created by the oscillating ions. The output current is transferred to the data acquisition board. It has an amplification factor of about 60 db and covers the frequency range from 15 khz to 10 MHz. The diagnostic LEDs on the preamplifier are listed in Table 1-3 on page 1-33. The positions of the diagnostic LEDs on the board are indicated by white rectangles in Figure 1-25. 1 Part number of complete unit. 1-32 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Functional Description Printed Circuit Boards Table 1-3. Diagnostic LEDs on the Preamplifier board No. Name Color Description Normal Operating Condition LD1 Overload Yello w RF output is overloaded Off LD2 +5 V Green +5 V input voltage present On LD3 +15 V Green +15 V input voltage present On LD4-5 V Green -5 V input voltage present On LD5 Input off Yello w RF inputs are shortened (protection) On, off during Detect Internal Computer Figure 1-26 shows the components of the data acquisition unit (P/N 206 4132). The unit is mounted in a housing located at the right side of the instrument. Power Supply 2 board Location of Data Acquisition Analog board Data Acquisition Digital PCI board Computer housing Instrument Control board Figure 1-26. Data Acquisition unit (covers removed) The internal computer (P/N 207 6470) contains a computer mainboard with an ATX power supply. The data acquisition digital PCI board is directly plugged into the mainboard. The data acquisition analog board is mounted on top of the computer mainboard. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-33

Functional Description Printed Circuit Boards Data Acquisition Digital PCI Board Figure 1-27 shows the data acquisition digital PCI board (P/N 206 0501). It is an add-on board to the internal computer (See Figure 1-26 on page 1-33.). Figure 1-27. Data Acquisition Digital PCI board This board is used to convert detected ion signals to digital form and to interface to the computer mainboard. The board has two 16 bit parallel connections to the DAC and the ADC on the data acquisition analog board, which is used for controlling and reading-back signals. A high-speed link port channel is also on the board that is used to communicate with the electronics in the linear ion trap. While precision timing is derived from the data acquisition analog board, events with lower requirements use the timer in the internal computer. This timer is used to check at regular intervals whether the foreground process works as expected. Communication takes place not only between the ion trap and the internal computer of the LTQ Orbitrap Discovery system, but also between the ion trap and the data system computer. For further information about the data system, refer to the LTQ XL Hardware Manual. The diagnostic LEDs listed in Table 1-4 on page 1-35 show the status of the board. The position of the LEDs on the board is indicated by a white rectangle in Figure 1-27. 1-34 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Functional Description Printed Circuit Boards Table 1-4. Diagnostic LEDs of the Data Acquisition Digital PCI board Name Color Description Normal Operating Condition +5 V Green +5 V voltage present On +3.3 V Green +3.3 V voltage present On +2.5 V Green +2.5 V voltage present On Data Acquisition Analog Board Figure 1-28 shows the data acquisition analog board (P/N 206 4150). Figure 1-28. Data Acquisition Analog board This board is an add-on board to the mainboard of the internal computer. See Figure 1-26 on page 1-33. It is used to convert analog to digital signals for Orbitrap experiments, especially for detecting the ions. The board contains an ADC for the detection of the transient signal, with a frequency range from 10 khz to 10 MHz. Three anti-aliasing filters for the low, middle and high mass range are automatically selected by the software. The data acquisition board provides precision timing to control the acquisition. Events with lower timing requirements on accuracy are controlled by the linear ion trap. The diagnostic LEDs listed in Table 1-5 on page 1-36 show the status of the voltages applied to the board. The position of the LEDs on the board is indicated by a white rectangle in Figure 1-28. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-35

Functional Description Printed Circuit Boards Table 1-5. Diagnostic LEDs of the Data Acquisition Analog board Name Color Description Normal Operating Condition +5 V Green +5 V voltage present On -5 V Green -5 V voltage present On +3.3 V Green +3.3 V voltage present On Power Supply 2 Board The power supply 2 board (P/N 206 1440) provides the supply voltages for the data acquisition analog board. It is mounted to the back inside the housing of the internal computer. See Figure 1-26 on page 1-33. The diagnostic LEDs listed in Table 1-6 show the status of the voltages applied to the board. Table 1-6. Diagnostic LEDs of the Power Supply 2 board Name Color Description Normal Operating Condition +5.1 V Green +5.1 V voltage present On -5.1 V Green -5.1 V voltage present On +3.3 V Green +3.3 V voltage present On Instrument Control Board Figure 1-29 shows the instrument control board (P/N 205 4221). The instrument control board is located in a housing next to the internal computer. It is connected to the LTQ Orbitrap Discovery main power. The instrument control board is used to interface the LTQ XL control electronics to the Orbitrap control electronics. Three signal lines are passed from the LTQ XL: a digital, parallel (DAC) bus, a serial SPI bus, and a Link Port Signal line. The instrument control board contains a micro controller, digital and analog converters, and serial port connectors. On the instrument control board, analog signals from vacuum gauges are converted to digital signals and passed to the data system as well as to the power distribution board. (See page 1-38.) Turbopumps (Refer to the topic Vacuum System on page 1-19.) are attached to a serial port connector and this is connected via the signal lines to the linear ion trap. 1-36 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Functional Description Printed Circuit Boards Diagnostic LEDs Status LEDs Figure 1-29. Instrument Control board The diagnostic LEDs listed in Table 1-7 show the status of applied voltages to the board. The position of the diagnostic LEDs on the board is indicated by a white rectangle in Figure 1-29. Table 1-7. Diagnostic LEDs of the Instrument Control board No. Name Color Description Normal Operating Condition LD1 2.5 V Green 2.55 V Input voltage present On LD2 3.3 V Green 3.3 V Input voltage present On LD3 5 V Green 5 V Input voltage present On LD4-15 V Green -15 V Input voltage present On LD5 +15 V Green +15 V Input voltage present On Additionally, the board has four green LEDs that are directly connected to the micro controller. They indicate the state of the micro controller and possible error bits and can be used for software debugging. See Table 1-8 on page 1-38. The position of the status LEDs on the board is indicated by a white oval in Figure 1-29 on page 1-37. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-37

Functional Description Printed Circuit Boards Table 1-8. Software status LEDs of the Instrument Control board No. Description Normal Operating Condition 6.1 Micro controller is working properly Permanent flashing of LED 6.2 CAN bus connection to power distribution board enabled On 6.3 Connection to internal computer and LTQ XL SPI bus enabled 6.4 Orbitrap SPI bus enabled On Flashing on error On Power Distribution Board Figure 1-30 on page 1-38 shows the power distribution board (P/N 210 1320) 1. It is located at the bottom of the right side of the instrument. Figure 1-30. Power Distribution board 1 Part number of complete unit. 1-38 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Functional Description Printed Circuit Boards The power distribution board controls the vacuum system and the system power supplies, including the linear ion trap. Depending on the quality of the vacuum and the status of the turbo molecular pumps, it switches the vacuum gauges, the pumps, and the 230 V relays. It controls external relays with 24 V dc connections. In case of a vacuum failure, it initiates an automatic power down of the instrument. The board also switches the valve that controls the flow of the HCD collision gas. The power distribution board indicates all system states and error messages by status LEDs (see Table 1-9 on page 1-40) in the middle of the left side of the board. A green LED indicates that the status is OK. An orange LED indicates a status that differs from normal. The position of the LEDs on the board is indicated by a white oval in Figure 1-30 on page 1-38. The system status LEDs on the front side of the instrument (See Figure 1-4 on page 1-6.) are controlled by the power distribution board. The information partially comes from external boards (for example, the Communication LED is controlled by the instrument control board). (Refer to topic Instrument Control Board on page 1-36.) Diagnostic LEDs show the status of voltages applied from the board to other devices. The positions of the diagnostic LEDs on the board are indicated by white rectangles in Figure 1-30 on page 1-38. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-39

Functional Description Printed Circuit Boards Table 1-9. Status LEDs of the Power Distribution board LED green LED orange Information given by orange LED Vacuum High vacuum failure High vacuum pressure > 10-8 mbar Comm. No communication with instrument control board CAN bus problem or instrument control board not working System System is not ready FT Electronics switch off or Vacuum Pumps switch off Scan Instrument is not scanning Electr. On Service mode FT Electronics switch off Vac. Units Ok Vacuum measurement failure Vacuum gauge defective Pirani Orbitrap Ok No function, at present Pirani LT Ok Pirani LTQ XL failure Control signal < 0.5 V Ion Gauge ON Penning LTQ Orbitrap Discovery off Forevacuum > 10-2 mbar Ion Gauge OK Penning LTQ Orbitrap Discovery failure Control signal < 0.5 V LT Vacuum Work LTQ XL vacuum failure Vacuum forepump LTQ XL >10-1 mbar Vac. <10-3 Forevacuum failure Forevacuum > 10-3 mbar Vac. <10-5 High vacuum failure High vacuum > 10-5 mbar Pumps OK Pumps Off Pump down; leakage Rough P. 1 ON Forepump #1 failure Forepump defective Turbo P. 1 ON Turbopump #1 failure Turbopump defective/error * Rotation 1 OK Turbopump #1 failure 80% rotation speed of turbopump not reached Turbo P. 2 ON Turbopump #2 failure Turbopump defective/error * Rotation 2 OK Turbopump #2 failure 80% rotation speed of turbopump not reached Heater Off Heater enabled Heater enabled LAN Conn. Ok LAN connection failure LAN interrupted (Option) EI ON No function, at present A System reset System reset has occured B Micro controller idle * An error of turbopump 3 is indicated by an LED directly located on the pump controller. 1-40 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Functional Description Printed Circuit Boards Depending on user actions, the power distribution is switched to various working modes by the hardware. See Table 1-10. Table 1-10. Working modes of the Power Distribution board Action Consequences a. Main switch off Complete system including linear ion trap and multiple socket outlets (data system, for example) are without power b. Vacuum Pumps switch off Everything is switched off c. FT Electronics switch off All components are switched off with exception of the following ones: Heater control Multiple socket outlets Power distribution board Pumps Vacuum control LTQ XL (has a separate Service switch) Table 1-11 shows the possible operating states of the power distribution. Table 1-11. Operating states of the Power Distribution board Action 1. Main switch on, Vacuum Pumps switch off 2. Vacuum Pumps switch on and FT Electronics switch on 3. Check linear ion trap and LTQ Orbitrap Discovery forevacuum pump: 10-0 mbar after 30 s 4. After the system has started, the Pirani gauge returns a vacuum < 10-2 mbar and both turbopumps reach 80% rotation speed 5. Vacuum and 80% rotation speed of turbopumps not reached after preset time (< 8 min, otherwise the pumps automatically switch off) 6. One or more vacuum gauges defective (control signal < 0.5 V) Consequences Everything is switched off System starts up: pumps and electronics switched on If not ok: switch off system and light error LED * ; power distribution remains switched on Switch on Penning gauge Switch off system (including linear ion trap) and light error LED * ; power distribution remains switched on Light error LED only, otherwise ignore Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-41

Functional Description Printed Circuit Boards Table 1-11. Operating states of the Power Distribution board, continued Action 7. After the operating status is reached, the pressure at one gauge exceeds the security threshold for more than the preset time period: Pirani gauge LTQ Orbitrap Discovery >10-1 mbar Penning gauge LTQ Orbitrap Discovery >10-3 mbar Pirani gauge LT forepump >10-1 mbar 8. Rotation speed of a turbopump falls below 80% System is shut down with exception of power distribution (light error LED). Rebooting of the system by switching off/on of the main switch. Shut down system (see 7.); light LED * of corresponding pump 9. Service switch linear ion trap off Linear ion trap electronics switched off, pumps keep on running; LTQ Orbitrap Discovery without data link, keeps on running 10. FT Electronics switch LTQ Orbitrap Discovery off 11. Failure of linear ion trap or LTQ Orbitrap Discovery (e.g. fuse is opened) Consequences LTQ Orbitrap Discovery electronics switched off, pumps keep on running; LTQ Orbitrap Discovery without data link, keeps on running If the vacuum in one part deteriorates, the complete system is shut down. 12. Mains failure System powers up after the electricity is available again. All devices reach the defined state. Linear ion trap and internal computer must reboot. * After the shutdown, the LED flashes that represents the reason for the shutdown. Power Supply 1 Board Figure 1-31 on page 1-43 shows the power supply 1 board (P/N 205 5810). This board is located next to the power distribution board. It provides the power for the ion optic supply board (Refer to topic Ion Optic Supply Board on page 1-45.) and the instrument control board. (Refer to topic Instrument Control Board on page 1-36.) 1-42 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Functional Description Printed Circuit Boards Figure 1-31. Power Supply 1 board Warning Parts of the power supply 1 board are at high voltage. The diagnostic LEDs listed in Table 1-12 show the status of the voltages applied to the board. The position of the LEDs on the board is indicated by the white rectangles in Figure 1-31. Table 1-12. Diagnostic LEDs of the Power Supply 1 board Name Color Description Normal Operating Condition +285 V Green +285 V Output voltage present On -285 V Green -285 V Output voltage present On Over Current +285 V Red LED lit dark red: I out > 80 ma LED lit bright red: output is short-circuited Off Over Current -285 V Red LED lit dark red: I out > 80 ma LED lit bright red: output is short-circuited +18 V Green +18 V Output voltage present On -18 V Green -18 V Output voltage present On +8.5 V Green +8.5 V Output voltage present On Off Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-43

Functional Description Printed Circuit Boards Electronic Boards on the Left Side of the Instrument Figure 1-32 shows the left side of the instrument with the panel opened. This side of the instrument contains mostly boards that are part of the Orbitrap control. Ion Optic Supply board housing Central Electrode Pulser board Temperature Controller board CLT RF Main board RF Off & Feedback board Central Electrode Power Supply board High Voltage Power Supply board Figure 1-32. Electronic boards on the left side of the instrument The main components on this side are described starting from the top. 1-44 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Functional Description Printed Circuit Boards Ion Optic Supply Board Figure 1-33 shows the ion optic supply board (P/N 209 9810) 1. The board is located in a housing on top of the left instrument side of the instrument. This board supplies the voltages and the radio frequency for the ion guides and interoctapole lenses of the LTQ Orbitrap Discovery. It has an RF detector for the RF output control. The board also provides the trap voltage, gate voltage, and reflector dc voltages as well as the RF voltages to the octapole 1 of the Orbitrap. See topic Orbitrap Analyzer on page 1-13 for further information. Furthermore, the board provides the voltages for the HCD collision cell. 2 See page 1-17. Figure 1-33. Ion Optic Supply board The diagnostic LEDs listed in Table 1-13 on page 1-46 show the status of applied voltages to the board. The position of the LEDs on the board is indicated by white rectangles in Figure 1-33. Warning Parts of the board are at high voltage. 1 Part number of complete unit. 2 HCD is an option for LTQ Orbitrap Discovery. The feature will be not available if the instrument is not equipped with this option. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-45

Functional Description Printed Circuit Boards Table 1-13. Diagnostic LEDs of the Ion Optic Supply board No. Name Color Description Normal Operating Condition LD1 +275 V Green +275 V Input voltage present On LD2-275 V Green -275 V Input voltage present LD3 +29 V Green +29 V Input voltage present On LD5 +15 V Green +15 V Input voltage present On LD6-15 V Green -15 V Input voltage present On LD7 RF1_ON Blue RF1 generator switched on depending on application; LED flashes during scanning LD8 RF2_ON Blue RF2 generator switched on depending on application; LED flashes during scanning On Central Electrode Pulser Board The central electrode pulser board (P/N 207 9640) 1 is located in a housing that is mounted to the flange of the UHV chamber. Figure 1-34. Central Electrode Pulser board 1 Part number of complete unit. 1-46 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Functional Description Printed Circuit Boards The board switches the injection and measurement voltages for the central electrode and the detection electrodes of the Orbitrap. Resistor-capacitor circuits on the board convert the switching pulse into a smooth transition between the voltages. The diagnostic LEDs listed in Table 1-14 show the status of the voltages applied to the board as well as some operating states. The position of the LEDs on the board is indicated by the white rectangles in Figure 1-34 on page 1-46. Table 1-14. Diagnostic LEDs of the Central Electrode Pulser board No. Name Color Description Normal Operating Condition LD1 TRIG Green Trigger signal indicator Flashing when scanning LD2 PS Green 24V Power Supply is OK On Temperature Controller Board The temperature controller board (P/N 207 8930) is located on the top left side of the instrument, next to the CLT RF main board. See Figure 1-32 on page 1-44. The temperature controller board keeps the temperature of the analyzer chamber to a preset value. A Peltier element that can be used for heating as well as for cooling is used as an actuator. Activation is done via the serial SPI (Serial Peripheral Interface) bus. Figure 1-35. Temperature Controller board Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-47

Functional Description Printed Circuit Boards The diagnostic LEDs listed in Table 1-15 show the status of the voltages applied to the board as well as some operating states. The positions of the LEDs on the board are indicated by the white rectangles in Figure 1-35. Table 1-15. Diagnostic LEDs of the Temperature Controller board No. Name Color Description Normal Operating Condition LD1 +15 V Green +15 V Input voltage present On LD2-15 V Green -15 V Input voltage present On LD3 TEC >60C Yellow Temperature of cold side Peltier element above 60 ºC Off LD4 Unit >60C Yellow Temperature of UNIT heat sink above 60 ºC LD5 Reg Off Yellow Control switched off Off LD6 No Term Yellow SPI bus termination board Off missing LD7 SDT enable Green Interface has been addressed and sends/receives data Off Flashing on SPI bus data transfer LD8 SEL Green Board has been addressed Flashing on SPI bus data transfer LD9 Heating Yellow Peltier element is heating Depending on system state LD10 Cooling Yellow Peltier element is cooling Depending on system state LD11 UR>0 Yellow Summation voltage controller >0 V Off when adjusted LD12 UR<0 Yellow Summation voltage controller <0 V Off when adjusted CLT RF Unit The CLT RF unit (P/N 207 9581) comprises the CLT RF main board and the RF off & feedback board. The unit operates the curved linear trap (C-Trap) with four phases RF voltage and three pulsed DC voltages (PUSH, PULL, and OFFSET). The CLT RF main board (P/N 207 9591) is located in a housing in the center of the left side of the instrument. See Figure 1-32 on page 1-44. This board provides an RF voltage ( Main RF ) for the curved linear trap (C-Trap). It allows switching off the RF and simultaneous pulsing of each C-Trap electrode. See topic Orbitrap Analyzer on page 1-13 for further information. The board communicates with the instrument control board via an SPI bus. The RF off & feedback board (P/N 208 2540) is an add-on board to the CLT RF main board. It is located in the same housing. See Figure 1-36 on page 1-49. 1-48 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Functional Description Printed Circuit Boards RF off & feedback board Figure 1-36. CLT RF unit (cover removed) The diagnostic LEDs listed in Table 1-16 show the status of the voltages applied to the board as well as some operating states. The position of the LEDs on the board is indicated by the white rectangles in Figure 1-36. Table 1-16. Diagnostic LEDs of the CLT RF Main board No. Name Color Description Normal Operating Condition LD1 NO TERM Yellow SPI bus termination board missing Off LD2 SEND Yellow Interface has been addressed and sends/receives data Flashing on SPI-bus data transfer LD3 SEL Green Board has been addressed Flashing on SPI-bus data transfer LD4 RF ON Green RF voltage on On LD5 NO LOCK Yellow PLL has been not locked 50% intensity LD6 OVL Yellow RF Amplifier overload Off LD7 OVHEAT Red Heatsink temperature > 73 C Off Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-49

Functional Description Printed Circuit Boards Central Electrode Power Supply Board The central electrode power supply board (P/N 207 9611) 1 is mounted in a housing on the bottom left side of the instrument. See Figure 1-37. Figure 1-37. Central Electrode Power Supply board The board supplies four dc voltages to the Orbitrap: Two central electrode (CE) voltages: CE HIGH and CE LOW Two deflector electrode (DE) voltages: DE HIGH and DE LOW. For positive ions, the CE voltages are negative and the DE voltages are positive. The maximum CE voltage is 3 kv and the maximum DE voltage is 1 kv. The board communicates via the SPI bus. In addition to a ventilator on the bottom right side, a water-cooled Peltier element on the rear side of the board serves as means of heat dissipation. 1 Part number of complete unit. 1-50 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Functional Description Printed Circuit Boards The diagnostic LEDs listed in Table 1-17 on page 1-51 show the status of the voltages applied to the board as well as some operating states. The position of the LEDs on the board is indicated by the red rectangles in Figure 1-37. Table 1-17. Diagnostic LEDs of the Central Electrode Power Supply board No. Name Color Description Normal Operating Condition LD1 OVL DE HI- Yellow Negative side of Deflector High Supply has been overloaded LD2 OVL DE HI+ Yellow Positive side of Deflector High Supply has been overloaded LD3 No Term Red SPI bus termination board missing LD4 Send Yellow Interface has been addressed and sends/receives data Off when HV is switched on Off when HV is switched on Off Flashing on SPI-bus data transfer LD5 Sel Green Board has been addressed Flashing on SPI-bus data transfer LD6 Polarity Blue Positive/negative ion mode Off (positive mode) LD7 OVL CE LO+ Yellow Positive side of Central Electrode Low Supply has been overloaded LD8 OVL CE LO- Yellow Negative side of Central Electrode Low Supply has been overloaded LD9 OVL CE HI+ Yellow Positive side of Central Electrode High Supply has been overloaded. LD10 OVL CE HI- Yellow Negative side of Central Electrode High Supply has been overloaded LD11 OVL DE LO+ Yellow Positive side of Deflector Low Supply has been overloaded. LD12 OVL DE LO- Yellow Negative side of Deflector Low Supply has been overloaded. Off when HV is switched on Off when HV is switched on Off when HV is switched on Off when HV is switched on Off when HV is switched on Off when HV is switched on LD13 HV ON Green High voltage switched on On when HV is switched on High Voltage Power Supply Board The high voltage power supply board (P/N 207 7991) 1 is mounted in a housing on the bottom left side of the instrument. See Figure 1-32 on page 1-44. This board provides five dc voltages for the ion optics of the LTQ Orbitrap Discovery. Two voltages supply the lenses of the instrument. Three voltages are applied to the RF CLT main board to be 1 Part number of complete unit. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-51

Functional Description Printed Circuit Boards used as focusing potentials for the curved linear trap. See topic Orbitrap Analyzer on page 1-13 for further information. The board communicates via the SPI bus. Warning The high voltage power supply board creates voltages up to 3.5 kv! Figure 1-38. High Voltage Power Supply board (cover removed) The diagnostic LEDs listed in Table 1-18 on page 1-53 show the operating states of the board. The position of the LEDs on the board is indicated by the white rectangles in Figure 1-38. 1-52 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Functional Description Printed Circuit Boards Table 1-18. Diagnostic LEDs of the High Voltage Power Supply board No. Name Color Description Normal Operating Condition LD1 NO TERM Red SPI bus termination board missing Off LD2 SEND Yellow Interface has been addressed and sends/receives data Flashing on SPI bus data transfer LD3 SEL Green Board has been addressed Flashing on SPI bus data transfer LD4 HV ON Green High voltage is switched on On LD5 POLARITY Green Positive/negative ion mode Off (positive mode) SPI Bus Termination Board Various boards communicate via the SPI bus, a serial RS485-based bus system. The SPI bus termination board reduces unwanted signal reflections. The boards indicate a missing termination (after maintenance, for example) by LEDs. The SPI bus termination board (P/N 208 1480) is located at the bottom left side of the instrument, below the high voltage power supply board. See Figure 1-39. SPI bus termination board Figure 1-39. High Voltage Power Supply board with SPI Bus Termination board Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 1-53

Chapter 2 Basic System Operations Many maintenance procedures for the LTQ Orbitrap Discovery system require that the MS detector be shut down. In addition, the LTQ Orbitrap Discovery system can be placed in Standby condition if the system is not to be used for 12 h or more. The following topics are discussed in this chapter: Shutting Down the System in an Emergency on page 2-2 Placing the System in Standby Condition on page 2-4 Shutting Down the System on page 2-5 Starting Up the System after a Shutdown on page 2-7 Resetting the System on page 2-10 Resetting the Tune and Calibration Parameters to their Default Values on page 2-11 Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 2-1

Basic System Operations Shutting Down the System in an Emergency Shutting Down the System in an Emergency If you need to turn off the MS detector in an emergency, place the main power switch (located on the power panel at the right side of the LTQ Orbitrap Discovery) in the Off (O) position. This turns off all power to the instrument, including the linear ion trap, multiple socket outlets for the data system, and the vacuum pumps. The main power switch must be turned 90 anti-clockwise to switch off the instrument. See Figure 2-1. On Off Figure 2-1. Main power switch in Off position The instrument is automatically vented by the vent valve of the linear ion trap. The vent valve vents the system 30 s after power is switched off. Although removing power abruptly will not harm any component within the system, this is not the recommended shutdown procedure to follow. Refer to topic Shutting Down the System on page 2-5 for the recommended procedure. Note To separately turn off the recirculating chiller or computer in an emergency, use the On/Off switches on the chiller and computer, respectively. Behavior of the System in Case of a Main Failure A main power failure has the same consequence as switching off via the main power switch. If the power is available again, the system is started up automatically i.e. the pumps are switched on and the vacuum is created. If the system has been vented during the mains failure, it is necessary to bakeout the system to obtain the operating vacuum. Refer to the topic Baking Out the System on page 3-4. It is not possible to check whether the system was vented. The log file of the data system indicates a reboot of the system. In case of frequent but short power failures we recommend installing an uninterruptible power 2-2 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Basic System Operations Shutting Down the System in an Emergency supply (UPS). If main power failures occur frequently while the system is not attended (e.g. in the night), we recommend installing a power fail detector. Note The intentional venting of the system is performed with the vent valve of the linear ion trap. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 2-3

Basic System Operations Placing the System in Standby Condition Placing the System in Standby Condition The LTQ Orbitrap Discovery system should not be shut down completely if you are not going to use it for a short period of time, such as overnight or over the weekend. When you are not going to operate the system for 12 hours or more, you can leave the system in Standby condition. Use the following procedure to place the LTQ Orbitrap Discovery system in the Standby condition: 1. Wait until data acquisition, if any, is complete. 2. Turn off the flow of sample solution from the LC (or other sample introduction device). Note For instructions on how to operate the LC from the front panel, refer to the manual that came with the LC. 3. From the Tune Plus window, choose Control > Standby (or click on the On/Standby button to toggle it to Standby) to put the instrument in Standby condition. The consequences of this user action are described in the LTQ XL Hardware Manual. The System LED on the front panel of the LTQ XL is illuminated yellow when the system is in Standby condition. 4. Leave the LC power On. 5. Leave the autosampler power On. 6. Leave the data system power On. 7. Leave the LTQ Orbitrap Discovery main power switch in the On position. 2-4 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Basic System Operations Shutting Down the System Shutting Down the System The LTQ Orbitrap Discovery system does not need to be shut down completely if you are not going to use it for a short period of time, such as overnight or over a weekend. Refer to the topic Placing the System in Standby Condition on page 2-4. This section describes how to shut down the system for a maintenance or service procedure. Use the following procedure to shut down the LTQ Orbitrap Discovery system: 1. Wait until data acquisition, if any, is complete. 2. Turn off the flow of sample solution from the LC (or other sample introduction device). Note For instructions on how to operate the LC from the front panel, refer to the manual that came with the LC. 3. From the Tune Plus window, choose Control > Off to put the instrument in Off condition. When you choose Control > Off, all high voltages are shut off, as are the sheath and auxiliary gas. 4. Put the FT Electronics switch to the OFF position. See Figure 1-7 on page 1-9. 5. Put the Vacuum Pumps switch to the OFF position. See Figure 1-7. When you place the switch in the OFF position, the following occurs: a. All power to the instrument, including the turbomolecular pumps and the rotary-vane pumps, is turned off. b. After 30 s, power to the vent valve solenoid of the ion trap is shut off. The vent valve opens and the vacuum manifold is vented with nitrogen to atmospheric pressure through a filter. You can hear a hissing sound as the gas passes through the filter. 6. Leave the main power switch of the LTQ Orbitrap Discovery in the On position. 7. During service or maintenance operations that require opening the vacuum system of the LTQ XL or LTQ Orbitrap Discovery, always put the main switch (main circuit breaker) to the OFF position. You Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 2-5

Basic System Operations Shutting Down the System can secure the main switch with a padlock or tie-wrap to prevent unintended re-powering. Warning Allow heated components to cool before you service them (the ion transfer tube at about 300 C, for example). Note If you are planning to perform routine or preventive system maintenance on the LTQ Orbitrap Discovery only, you do not need to turn off the recirculating chiller, LC, autosampler, or data system. In this case, the shutdown procedure is completed. However, if you do not plan to operate your system for an extended period of time, you might want to turn off the recirculating chiller, LC, autosampler, and data system. 2-6 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Basic System Operations Starting Up the System after a Shutdown Starting Up the System after a Shutdown To start up the LTQ Orbitrap Discovery after it has been shut down, you need to do the following: 1. Start up the instrument 2. Set up conditions for operation Starting Up the Instrument Note The recirculating chiller and data system must be running before you start up the instrument. The instrument will not operate until software is received from the data system. Use the following procedure to start up the LTQ Orbitrap Discovery: 1. Start up the (optional) LC and autosampler as is described in the manual that came with the LC and autosampler. 2. Start up the data system and the chiller. 3. Turn on the flows of helium and nitrogen and argon if present at the tanks, if they are off. 4. Make sure that the main power switch of the LTQ XL is in the On position and the electronics service switch of the LTQ XL is in the Operating position. 5. Place the main power switch at the right side of the LTQ Orbitrap Discovery in the On position. 6. Put the Vacuum Pumps switch to the ON position. See Figure 1-7 on page 1-9. The rotary-vane pumps and the turbomolecular pumps are started. Note Pumping the system after a complete shut down takes hours and requires overnight baking of the system. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 2-7

Basic System Operations Starting Up the System after a Shutdown 7. Put the FT Electronics switch to the ON position. See Figure 1-7. When you place the FT Electronics switch to the ON position, the following occurs: a. Power is provided to all electronic boards. (The electron multiplier, conversion dynode, 8 kv power to the API source, main RF voltage, and octapole RF voltage remain off.) b. The internal computer reboots. After several seconds, the Communication LED on the front panel is illuminated yellow to indicate that the data system has started to establish a communication link. c. After several more seconds, the Communication LED is illuminated green to indicate that the data system has established a communication link. Software for the operation of the instrument is then transferred from the data system to the instrument. d. After 3 min, the System LED of the ion trap is illuminated yellow to indicate that the software transfer from the data system is complete and that the instrument is in Standby condition. Note The Vacuum LED on the front panel of the LTQ XL is illuminated green only if the pressure in the vacuum manifold is below the maximum allowable pressure (5 10-4 Torr in the analyzer region, and 2 Torr in the capillary-skimmer region), and the safety interlock switch on the API source is depressed (that is, the API flange is secured to the spray shield). 8. Press the Reset button on the LTQ XL to establish the communication link between LTQ XL and internal computer. If you have an LC or autosampler, start it as is described in the manual that came with the LC or autosampler. If you do not have either, go to the topic Setting Up Conditions for Operation below. Setting Up Conditions for Operation Set up your LTQ Orbitrap Discovery for operation, as follows: 1. Before you begin data acquisition with your LTQ Orbitrap Discovery system, you need to allow the system to pump down for at least 8 hours. Operation of the system with excessive air and water in the vacuum manifold can cause reduced sensitivity, tuning problems, and a reduced lifetime of the electron multiplier. Note The vacuum in the analyzer system can be improved by an overnight baking of the system. Refer to the topic Baking Out the System on page 3-4. 2-8 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Basic System Operations Starting Up the System after a Shutdown 2. Ensure that the gas pressures are within the operational limits: Helium: 275 ± 70 kpa (2.75 ± 0.7 bar, 40 ±10 psi), Nitrogen: 690 ± 140 kpa (6.9 ± 1.4 bar, 100 ± 20 psi). Argon if present: 690 ± 140 kpa (6.9 ± 1.4 bar, 100 ± 20 psi) Note Air in the helium line must be purged or given sufficient time to be purged for normal performance. 3. Select the Display Status View button in the Tune Plus window. Check to see whether the pressure measured by the ion gauge is 5 10-9 mbar, and the pressure measured by the Pirani gauge is around 1 mbar. Compare the values of the other parameters in the status panel with values that you recorded previously. 4. Continue to set up for ESI or APCI operation as described in LTQ Orbitrap Discovery Getting Started manual. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 2-9

Basic System Operations Resetting the System Resetting the System If communication between the LTQ Orbitrap Discovery and data system computer is lost, it may be necessary to reset the system using the Reset button of the LTQ XL. The procedure given here assumes that the LTQ Orbitrap Discovery and data system computer are both powered on and are operational. If the instrument, data system computer, or both are off, refer to topic Starting Up the System after a Shutdown on page 2-7. To reset the LTQ Orbitrap Discovery, press the Reset button of the linear ion trap. See the LTQ XL Hardware Manual for the location of the Reset button. When you press the Reset button, the following occurs: 1. An interrupt on the mainboard of the internal computer causes the internal computer to reboot. All LEDs on the front panel are off except the Power LED. 2. After several seconds, the Communication LED is illuminated yellow to indicate that the data system and the instrument are starting to establish a communication link. 3. After several more seconds, the Communication LED is illuminated green to indicate that the data system and the instrument have established a communication link. Software for the operation of the instrument is then transferred from the data system to the instrument. 4. After 3 min, the software transfer is complete. The System LED is illuminated either green to indicate that the instrument is functional and the high voltages are on, or yellow to indicate that the instrument is functional and it is in Standby condition. 2-10 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

Basic System Operations Resetting the Tune and Calibration Parameters to their Default Values Resetting the Tune and Calibration Parameters to their Default Values You can reset the LTQ Orbitrap Discovery system tune and calibration parameters to their default values at any time. This feature may be useful if you have manually set some parameters that have resulted in less than optimum performance. To reset the LTQ Orbitrap Discovery tune and calibration parameters to their default values, proceed as follows: In the Tune Plus window, Choose File > Restore Factory Calibration to restore the default calibration parameters, or Choose File > Restore Factory Tune Method to restore the default tune parameters. Note Make sure that any problems you might be experiencing are not due to improper API source settings (spray voltage, sheath and auxiliary gas flow, ion transfer capillary temperature, etc.) before resetting the system parameters to their default values. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 2-11

Chapter 3 User Maintenance This chapter describes routine maintenance procedures that must be performed to ensure optimum performance of the LTQ Orbitrap Discovery. It is the user s responsibility to maintain the system properly by performing the system maintenance procedures on a regular basis. The following topics are described in this chapter: General Remarks on page 3-2 Baking Out the System on page 3-4 Maintaining the Vacuum System on page 3-6 Maintenance of the Recirculating Chiller on page 3-7 Note For instructions on maintaining the LTQ XL linear trap, refer to the LTQ XL Hardware Manual. For instructions on maintaining LCs or autosamplers, refer to the manual that comes with the LC or autosampler. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 3-1

User Maintenance General Remarks General Remarks Preventive maintenance must commence with installation, and must continue during the warranty period to maintain the warranty. Thermo Fisher Scientific offers maintenance and service contracts. Contact your local Thermo Fisher Scientific office for more information. Routine and infrequent maintenance procedures are listed in Table 3-1. Table 3-1. User maintenance procedures MS Detector Component Procedure Frequency Procedure Location Analyzer System bakeout If necessary (e.g. after performing maintenance work on the vacuum system) page 3-4 Rotary-vane pumps Add oil If oil level is low Manufacturer s documentation Change oil Every 3 months or if oil is cloudy or Manufacturer s documentation discolored Turbomolecular pumps Exchange lubricant reservoir Yearly Manufacturer s documentation page 3-6 Recirculating chiller Check cooling fluid level Check cooling fluid filter Check air inlet filter See manufacturer s documentation Manufacturer s documentation page 3-7 To successfully carry out the procedures listed in this chapter, observe the following: Proceed methodically Always wear clean, lint-free gloves when handling the components of the API source, ion optics, mass analyzer, and ion detection system. Always place the components on a clean, lint-free surface. Always cover the opening in the top of the vacuum manifold with a large, lint-free tissue whenever you remove the top cover plate of the vacuum manifold. Never overtighten a screw or use excessive force. Dirty tools can contaminate your system. Keep the tools clean and use them exclusively for maintenance and service work at the LTQ Orbitrap Discovery. Never insert a test probe (for example, an oscilloscope probe) into the sockets of female cable connectors on PCBs. Returning Parts In order to protect our employees, we ask you for some special precautions when returning parts for exchange or repair to the factory. Your signature on the Repair Covering letter confirms that the returned 3-2 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

User Maintenance General Remarks parts have been de-contaminated and are free of hazardous materials. Refer to topic Safety Advice for Possible Contamination on page vii for further information. Cleaning the Surface of the Instrument Clean the outside of the instrument with a dry cloth. For removing stains or fingerprints on the surface of the instrument (panels, for example), slightly dampen the cloth (preferably made of microfiber) with distilled water. Caution Prevent any liquids from entering the inside of the instrument. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 3-3

User Maintenance Baking Out the System Baking Out the System This section provides information and help concerning the system bakeout of the LTQ Orbitrap Discovery. The bakeout procedure removes unwanted gases or molecules (collected or remaining) from the high vacuum region of the instrument. Ions can collide with those gases or molecules resulting in lower overall sensitivity. Therefore, we recommend to bake out the instrument if the high vacuum decreases noticeable during routine operation. Bakeout is mandatory after maintenance or service work is performed in the analyzer region where the system is vented. Note Pumping down the system after venting takes at least 8 hours, and usually requires overnight baking of the system. In case the system has been vented during a power failure, it is necessary to bake out the system to obtain the operating vacuum. Refer to the topic Behavior of the System in Case of a Main Failure on page 2-2. Bakeout Procedure Use the following procedure to perform a system bakeout: 1. Place the system in Standby condition as described in the section Placing the System in Standby Condition on page 2-4. 2. Put the FT Electronics switch at the power control panel into the ON position. 3. Set the bakeout time by entering the desired time (hh:mm) with the up/down keys of the bakeout timer. See Figure 3-1. Elapsed time display Set time display Up keys Down keys Bakeout stop button Bakeout start button Figure 3-1. Bakeout timer 3-4 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

User Maintenance Baking Out the System 4. Start the bakeout procedure by pressing the green start button on the right. The LTQ Orbitrap Discovery indicates a running bakeout procedure by the flashing Vacuum and System LEDs on the front side of the instrument. See Figure 1-4 on page 1-6. You can stop a running bakeout procedure by pressing the orange reset/stop button on the left side. Also press this button after you have changed the preset bakeout time. 5. The bakeout procedure is terminated because of two reasons: The preset duration has expired, or The vacuum has risen above a preset value. The termination of the baking process is indicated by the status LEDs (System + Vacuum) on the front side that have stopped flashing. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 3-5

User Maintenance Maintaining the Vacuum System Maintaining the Vacuum System The turbopumps1 need maintenance work that is briefly outlined below. Note The manuals of the pump manufacturers give detailed advice regarding safety, operation, maintenance, and installation. Please note the warnings and precautions contained in these manuals! Exchanging the Lubricant Reservoir of the Turbopumps For all manipulations at the pumps, note the advice, warnings, and cautions contained in the pump manuals! For the turbopumps, we recommend exchanging the lubricant reservoir in a one-year cycle. At each exchange procedure, the complete lubricant reservoir must be exchanged! Note The storage stability of the lubrication oil is limited. The specification of durability is given by the pump manufacturer. (Refer to the manuals for the turbopumps.) Replacements for the turbopump lubricant reservoirs (TMH 071 P: P/N 017 2350; TMU 262: P/N 105 0160) are available from Thermo Fisher Scientific. The disposal of used oil is subject to the relevant regulations. 1 For maintenance of the forepumps, refer to the LTQ XL Hardware Manual or the pump manufacturer s manual. 3-6 LTQ Orbitrap Discovery Hardware Manual Thermo Fisher Scientific

User Maintenance Maintenance of the Recirculating Chiller Maintenance of the Recirculating Chiller For the NESLAB ThermoFlex 900 recirculating chiller, the following checks should be carried out on a regular basis. Note For further information and maintenance instructions, refer to the manufacturer s manual supplied with the instrument. Reservoir Periodically inspect the fluid inside the reservoir. If cleaning is necessary, flush the reservoir with a cleaning fluid compatible with the circulating system and the cooling fluid. The cooling fluid should be replaced periodically. Replacement frequency depends on the operating environment and amount of usage. Warning Before changing the operating fluid make sure it is at safe handling temperature. Fluid Bag Filter The ThermoFlex 900 recirculating chiller installed in the cooling circuit of the instrument is equipped with a fluid bag filter, which needs to be replaced on a regular basis. Replacement bags are available from Thermo Fisher Scientific. Condenser Filter To prevent a loss of cooling capacity and a premature failure of the cooling system, clean the condenser filter regularly. If necessary, replace it. Thermo Fisher Scientific LTQ Orbitrap Discovery Hardware Manual 3-7